//=============================================================================================================
/**
 * @file     coherence.cpp
 * @author   Daniel Strohmeier <Daniel.Strohmeier@tu-ilmenau.de>;
 *           Lorenz Esch <lesch@mgh.harvard.edu>
 * @version  dev
 * @date     April, 2018
 *
 * @section  LICENSE
 *
 * Copyright (C) 2018, Daniel Strohmeier, Lorenz Esch. All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without modification, are permitted provided that
 * the following conditions are met:
 *     * Redistributions of source code must retain the above copyright notice, this list of conditions and the
 *       following disclaimer.
 *     * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and
 *       the following disclaimer in the documentation and/or other materials provided with the distribution.
 *     * Neither the name of MNE-CPP authors nor the names of its contributors may be used
 *       to endorse or promote products derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
 * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
 * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
 * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * @note Notes:
 * - Some of this code was adapted from mne-python (https://martinos.org/mne) with permission from Alexandre Gramfort.
 *
 * @brief     Coherence class declaration.
 *
 */


//*************************************************************************************************************
//=============================================================================================================
// INCLUDES
//=============================================================================================================

#include "coherency.h"
#include "coherence.h"
#include "network/networknode.h"
#include "network/networkedge.h"
#include "network/network.h"
#include "../connectivitysettings.h"


//*************************************************************************************************************
//=============================================================================================================
// QT INCLUDES
//=============================================================================================================

#include <QDebug>
#include <QtConcurrent>


//*************************************************************************************************************
//=============================================================================================================
// Eigen INCLUDES
//=============================================================================================================

#include <unsupported/Eigen/FFT>


//*************************************************************************************************************
//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================

using namespace CONNECTIVITYLIB;
using namespace Eigen;


//*************************************************************************************************************
//=============================================================================================================
// DEFINE GLOBAL METHODS
//=============================================================================================================


//*************************************************************************************************************
//=============================================================================================================
// DEFINE MEMBER METHODS
//=============================================================================================================

Coherence::Coherence()
{
}


//*******************************************************************************************************

Network Coherence::calculate(ConnectivitySettings& connectivitySettings)
{
    Network finalNetwork("COH");

    if(connectivitySettings.isEmpty()) {
        qDebug() << "Coherence::calculate - Input data is empty";
        return finalNetwork;
    }

    if(AbstractMetric::m_bStorageModeIsActive == false) {
        connectivitySettings.clearIntermediateData();
    }

    finalNetwork.setSamplingFrequency(connectivitySettings.getSamplingFrequency());

    // Check if start and bin amount need to be reset to full spectrum
    int iNfft = connectivitySettings.getFFTSize();
    int iNFreqs = int(floor(iNfft / 2.0)) + 1;

    if(m_iNumberBinStart == -1 ||
       m_iNumberBinAmount == -1 ||
       m_iNumberBinStart > iNFreqs ||
       m_iNumberBinAmount > iNFreqs ||
       m_iNumberBinAmount + m_iNumberBinStart > iNFreqs) {
        qDebug() << "Coherence::calculate - Resetting to full spectrum";
        AbstractMetric::m_iNumberBinStart = 0;
        AbstractMetric::m_iNumberBinAmount = iNFreqs;
    }

    // Pass information about the FFT length. Use iNFreqs because we only use the half spectrum
    finalNetwork.setFFTSize(iNFreqs);
    finalNetwork.setUsedFreqBins(AbstractMetric::m_iNumberBinAmount);

    //Create nodes
    int rows = connectivitySettings.at(0).matData.rows();
    RowVectorXf rowVert = RowVectorXf::Zero(3);

    for(int i = 0; i < rows; ++i) {
        rowVert = RowVectorXf::Zero(3);

        if(connectivitySettings.getNodePositions().rows() != 0 && i < connectivitySettings.getNodePositions().rows()) {
            rowVert(0) = connectivitySettings.getNodePositions().row(i)(0);
            rowVert(1) = connectivitySettings.getNodePositions().row(i)(1);
            rowVert(2) = connectivitySettings.getNodePositions().row(i)(2);
        }

        finalNetwork.append(NetworkNode::SPtr(new NetworkNode(i, rowVert)));
    }

    //Calculate all-to-all coherence matrix over epochs
    Coherency::calculateAbs(finalNetwork,
                             connectivitySettings);;

    return finalNetwork;
}
